Hi Petr, thanks again for your reply. A colleague pointed out that the most likely alignment state of the (2nd) C is an insertion. It's located at the end of the read with just one more G after it and multiple Gs follow in the reference. The first C has at least two Gs following so that might make the indel state less likely. So this might be correct after all.
Andreas On 17 October 2014 21:02, Petr Danecek <p...@sanger.ac.uk> wrote: > Hi Andreas, > > On Fri, 2014-10-17 at 18:53 +0800, Andreas Wilm wrote: >> Hi Petr, >> >> thanks for your reply. With -x in samtools 1.0 some of the previously >> listed BAQ values change / get reduced and one 0 value is now at 36, >> but the one of interest (i.e the alternate C) still receives a zero: >> >> samtools 1.0 >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 36 38 38 38 37 34 34 77 >> 37 75 35 0 73 37 0 32 34 29 0 >> samtools 1.0 >> with -x >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 36 38 38 38 37 34 34 38 >> 37 39 35 39 38 37 35 32 34 29 36 >> >> The BAQ0 for the second C doesn't make sense to me, especially given >> the tview output (previously posted). > > Yes, it looks suspicious. I am not familiar enough with BAQ calculation > to give a useful answer, though. Maybe Heng could comment? > > >> Also, what does -x do? The manual says >> -x, --ignore-overlaps disable read-pair overlap detection >> Could you explain what this does and why it might affect BAQ computation? > > I believe it should not affect the calculation, only wanted to check > that the 0 quality isn't coming from somewhere else. > > Petr > > >> Andreas >> >> >> On 16 October 2014 19:21, Petr Danecek <p...@sanger.ac.uk> wrote: >> > Do you get the same output with -x? The base qualities are in set to 0, >> > so that we do not count reads of the same molecule twice. >> > >> > petr >> > >> > >> > On Mon, 2014-10-13 at 10:21 +0800, Andreas Wilm wrote: >> >> Hi all, >> >> >> >> every now and then I see BAQ values of 0 in samtools' mpileups. I >> >> thought I understood the overall concept, but now I'm not sure >> >> anymore. Does a value of 0 indicate this base is misaligned for sure? >> >> How can that ever be the case? Also, I see this happening in nicely >> >> aligned regions (all MQ60; not a lot of SNVs) with no indels anywhere >> >> nearby. It's seems to be mainly happening close to the end of reads >> >> and I see the same behaviour in samtools 0.1.19 and 1.0. >> >> >> >> Here's an example: how can the second C every get a BAQ of 0? >> >> >> >> Pileup information first (with base qualities translated into phred >> >> scores), followed by a screenshot of tview: >> >> >> >> # BAQ off >> >> >> >> samtools mpileup -B -Q 0 $BAM -f $REF -r chrX:46918110-46918110 >> >> >> >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 30 34 >> >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 >> >> >> >> # BAQ on >> >> >> >> samtools mpileup -Q 0 $BAM -f $REF -r chrX:46918110-46918110 >> >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 >> >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 >> >> >> >> # extended BAQ >> >> >> >> samtools mpileup -E -Q 0 $BAM -f $REF -r chrX:46918110-46918110 >> >> chrX 46918110 G 21 cc,c,,,,,.c.,,..,..., 4 0 >> >> 36 38 38 38 37 34 34 38 37 39 35 39 38 37 35 32 34 29 36 >> >> >> >> >> >> Screenshot of tview of the same region: >> >> https://dl.dropboxusercontent.com/u/4119940/baq0.png >> >> >> >> Can anyone explain this? >> >> >> >> Many thanks, >> >> >> >> Andreas >> >> >> >> PS: This was cross-posted on https://www.biostars.org/p/115071/#115112 >> >> >> > >> > >> > >> > >> > -- >> > The Wellcome Trust Sanger Institute is operated by Genome Research >> > Limited, a charity registered in England with number 1021457 and a >> > company registered in England with number 2742969, whose registered >> > office is 215 Euston Road, London, NW1 2BE. >> >> >> > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. -- Andreas Wilm andreas.w...@gmail.com | m...@andreas-wilm.com | 0x7C68FBCC ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
